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- PDB-2lo7: Ts16 NMR solution structure -

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Basic information

Entry
Database: PDB / ID: 2lo7
TitleTs16 NMR solution structure
ComponentsToxin Ts16
KeywordsTOXIN / CS ALPHA ALPHA MOTIF / ALPHA SCORPION TOXIN / VOLTAGE GATED POTASSIUM CHANNEL
Function / homologytoxin activity / extracellular region / Toxin Ts16
Function and homology information
Biological speciesTityus serrulatus (Brazilian scorpion)
MethodSOLUTION NMR / simulated annealing
Model detailsCS alfa alfa motif, model 1
Authorsdel Rio-Portilla, F. / Saucedo, A.L. / Flores-Solis, D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: New Tricks of an Old Pattern: STRUCTURAL VERSATILITY OF SCORPION TOXINS WITH COMMON CYSTEINE SPACING.
Authors: Saucedo, A.L. / Flores-Solis, D. / Rodriguez de la Vega, R.C. / Ramirez-Cordero, B. / Hernandez-Lopez, R. / Cano-Sanchez, P. / Navarro, R.N. / Garcia-Valdes, J. / Coronas-Valderrama, F. / de ...Authors: Saucedo, A.L. / Flores-Solis, D. / Rodriguez de la Vega, R.C. / Ramirez-Cordero, B. / Hernandez-Lopez, R. / Cano-Sanchez, P. / Navarro, R.N. / Garcia-Valdes, J. / Coronas-Valderrama, F. / de Roodt, A. / Brieba, L.G. / Possani, L.D. / Del Rio-Portilla, F.
History
DepositionJan 17, 2012Deposition site: BMRB / Processing site: RCSB
SupersessionMar 14, 2012ID: 2LKA
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Jan 15, 2014Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin Ts16


Theoretical massNumber of molelcules
Total (without water)3,4601
Polymers3,4601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20020 structures for lowest energy and no violations
RepresentativeModel #1no violations

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Components

#1: Protein/peptide Toxin Ts16 / Tityustoxin-16


Mass: 3460.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tityus serrulatus (Brazilian scorpion) / Strain: Ts16 / Production host: Escherichia coli (E. coli) / References: UniProt: P86271

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQFCOSY
121TOCSY
131NOESY
141NOESY

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Sample preparation

DetailsContents: 3.2 mM Ts16, 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 3.2 mM / Component: Ts16-1
Sample conditionspH: 3.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA5001
Varian VNMRSVarianVNMRS7002

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Processing

NMR softwareName: AMBER
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Amber force field
NMR representativeSelection criteria: no violations
NMR ensembleConformer selection criteria: 20 structures for lowest energy and no violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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